The more clearance the less the pump will be able to create suction on that side and pressure on the output. You can take the end plate, some wet/dry sand paper and a piece of glass. If you need a lot off to make it flat maybe some 200 grit, then move to finer and finer doing figure eights with the sandpaper on the glass to make it flat. Then you need to "set" the clearance on the gears to end cap. This needs to be tight like the main and rod clearances. You can adjust it with different thickness gaskets.